[R] Getting Sphericity Tests for Within Subject Repeated Measure Anova (using "car" package)
Sergios (Sergey) Charntikov
sergioschr at gmail.com
Tue Nov 10 03:20:33 CET 2009
Thank you very much. Finally got it to work. However, I had to recode it from:
columns: subject/treatment/DV (where all my response data was in one
DV column) to columns: subject/treatment/day1/day2/day3/ (where my
response data is now in three different columns).
Is there a way to do that without hand recoding (cutting and pasting
in spreadsheet) by hand? Thank you for your help. Glad it works as
is.
Sincerely,
Sergios Charntikov (Sergey), MA
Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 USA
On Mon, Nov 9, 2009 at 7:12 PM, John Fox <jfox at mcmaster.ca> wrote:
> Dear Sergios,
>
> Why don't you try what I suggested originally? Adapted to this data set,
>
> mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)
> idata <- data.frame(Day=factor(1:3))
> summary(Anova(mod, idata=idata, idesign=~Day))
>
> Peter Dalgaard also pointed toward an article that describes how to do the
> same thing with anova().
>
> Regards,
> John
>
>> -----Original Message-----
>> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
> On
>> Behalf Of Sergios (Sergey) Charntikov
>> Sent: November-09-09 7:13 PM
>> To: Mike Lawrence
>> Cc: r-help at r-project.org
>> Subject: Re: [R] Getting Sphericity Tests for Within Subject Repeated
> Measure
>> Anova (using "car" package)
>>
>> Hi Mike,
>>
>> I tried to run my data in SPSS and it works fine without any problems,
> plug
>> in my levels, plug in my covariate (since it is all within) and get my
>> Mauchly Tests.
>>
>> I tried to rearrange the data so it looks like this
>>
>> subj/treatment/day1/day2/day3
>>
>> subject treatment day1 day2 day3
>> 1 1 8 8 8
>> 1 2 5 7 5
>> 2 1 7 4 4
>> 2 2 4 5 7
>> 3 1 8 6 4
>> 3 2 5 2 4
>> 4 1 2 9 4
>> 4 2 1 9 1
>> 5 1 4 8 1
>> 5 2 7 8 2
>> 6 1 4 7 2
>> 6 2 4 5 2
>>
>>
>> When I try mlmfit <- lm(Dataset~1), I get "invalid type (list) for
> variable
>> 'Dataset"
>>
>> When I try
>>
>> mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)
>>
>> idata<- data.frame(factor(rep(c(Dataset$day1, Dataset$day2,
> Dataset$day3))),
>> ordered(Dataset$Treatment))
>>
>> Anova(mod, idata=idata, idesign=~Dataset$Treatment)
>>
>> I get: Terms in the intra-subject model matrix are not orthogonal.
>>
>> When I try is.matrix(Dataset) - I get no.
>>
>> My original mock Dataset (attached in txt) is below. Maybe I am not
> coding
>> it right? I would hate to recode all my data for SPSS, since at the end I
>> would need to show that Sphericity was not violated.
>>
>> Subj Trtmt Sessn Response
>>
>> 1 N 1 5
>>
>> 1 D 1 6
>>
>> 1 N 2 4
>>
>> 1 D 2 7
>>
>> 2 N 1 8
>>
>> 2 D 1 9
>>
>> 2 N 2 2
>>
>> 2 D 2 1
>>
>> 3 N 1 4
>>
>> 3 D 1 5
>>
>> 3 N 2 6
>>
>> 3 D 2 2
>>
>> 4 N 1 5
>>
>> 4 D 1 6
>>
>> 4 N 2 4
>>
>> 4 D 2 7
>>
>> 5 N 1 8
>>
>> 5 D 1 9
>>
>> 5 N 2 2
>>
>> 5 D 2 1
>>
>> 6 N 1 4
>>
>> 6 D 1 5
>>
>> 6 N 2 6
>>
>> 6 D 2 2
>>
>>
>>
>>
>> Sincerely,
>>
>> Sergios Charntikov (Sergey), MA
>>
>> Behavioral Neuropharmacology Lab
>> Department of Psychology
>> University of Nebraska-Lincoln
>> Lincoln, NE 68588-0308 USA
>>
>>
>>
>> On Mon, Nov 9, 2009 at 5:29 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
> wrote:
>> >
>> > No luck as in...? What error did you encounter?
>> >
>> > In your example data set, you only have 2 levels of each within-Ss
>> > factor, in which case you shouldn't expect to obtain tests of
>> > sphericity; as far as I understand it, sphericity necessarily holds
>> > when for repeated measures with only 2 levels and tests are really
>> > only possible for repeated measures with 3 or more levels.
>> >
>> > I think it's analogous to how you don't need to test homogeneity of
>> > variance when performing a paired t-test; the test ends up
>> > representing the pairs as single distribution of difference scores
>> > with a single variance.
>> >
>> > Mike
>> >
>> > On Mon, Nov 9, 2009 at 5:30 PM, Sergios (Sergey) Charntikov
>> > <sergioschr at gmail.com> wrote:
>> > > Tried EZanova, no luck with my particular dataset.
>> > >
>> > >
>> > > Sincerely,
>> > >
>> > > Sergios Charntikov (Sergey), MA
>> > >
>> > > Behavioral Neuropharmacology Lab
>> > > Department of Psychology
>> > > University of Nebraska-Lincoln
>> > > Lincoln, NE 68588-0308 USA
>> > >
>> > >
>> > >
>> > >
>> > > On Mon, Nov 9, 2009 at 2:25 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
>> wrote:
>> > >>
>> > >> Have you tried ezANOVA from the ez pacakge? It attempts to provide
>> > >> a simple user interface to car's ANOVA (and when that fails, aov).
>> > >>
>> > >> On Mon, Nov 9, 2009 at 1:44 PM, Sergios (Sergey) Charntikov
>> > >> <sergioschr at gmail.com> wrote:
>> > >> > Hello everyone,
>> > >> >
>> > >> > I am trying to do within subjects repeated measures anova
>> > >> > followed by the test of sphericity (sample dataset below).
>> > >> > I am able to get either mixed model or linear model anova and
>> > >> > TukeyHSD, but have no luck with Repeated-Measures Assuming
>> > >> > Sphericity or Separate Sphericity Tests.
>> > >> > I am trying to follow example from "car" package, but it seems
>> > >> > that I am not getting something right.
>> > >> >
>> > >> >> Dataset$Sessn <- as.factor(Dataset$Sessn)
>> > >> >
>> > >> >> LinearModel.1 <- lm(Response ~ Sessn*Trtmt, data=Dataset)
>> > >> >
>> > >> >> summary(LinearModel.1)
>> > >> >
>> > >> > All, good so far, but I have problem understanding "idata=" and
>> > >> > "idesign="
>> > >> > functions pertaining to my example. Session is my repeated
>> > >> > measure (Sessn 1 and Sessn 2 = two sessions, in reality I have
>> > >> > more) and it is already stacked. Any help or guidance on this
>> > >> > matter.
>> > >> >
>> > >> > Thank you, my mock dataset is below. Each subject has two levels
>> > >> > of treatment throughout four calendar days which are recoded to
>> > >> > Session 1 and Session 2 in order to compare treatments by the
>> > >> > first and subsequent days of exposure (Treatment x Session; my DV
>> > >> > is Response; Session is repeated).
>> > >> >
>> > >> > Subj Trtmt Sessn Response 1 N 1 5 1 D 1 6 1 N 2 4 1 D 2 7
>> > >> > 2 N 1
>> > >> > 8
>> > >> > 2 D 1 9 2 N 2 2 2 D 2 1 3 N 1 4 3 D 1 5 3 N 2 6 3 D 2 2 4
>> > >> > N 1 5
>> > >> > 4 D
>> > >> > 1 6 4 N 2 4 4 D 2 7 5 N 1 8 5 D 1 9 5 N 2 2 5 D 2 1 6 N 1
>> > >> > 4 6 D
>> > >> > 1 5
>> > >> > 6 N 2 6 6 D 2 2
>> > >> >
>> > >> > Sincerely,
>> > >> >
>> > >> > Sergios Charntikov (Sergey), MA
>> > >> >
>> > >> > Behavioral Neuropharmacology Lab
>> > >> > Department of Psychology
>> > >> > University of Nebraska-Lincoln
>> > >> > Lincoln, NE 68588-0308 USA
>> > >> >
>> > >> > sergioschr-at-gmail-dot-com
>> > >> >
>> > >> > [[alternative HTML version deleted]]
>> > >> >
>> > >> > ______________________________________________
>> > >> > R-help at r-project.org mailing list
>> > >> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > >> > PLEASE do read the posting guide
>> > >> > http://www.R-project.org/posting-guide.html
>> > >> > and provide commented, minimal, self-contained, reproducible code.
>> > >> >
>> > >> >
>> > >>
>> > >>
>> > >>
>> > >> --
>> > >> Mike Lawrence
>> > >> Graduate Student
>> > >> Department of Psychology
>> > >> Dalhousie University
>> > >>
>> > >> Looking to arrange a meeting? Check my public calendar:
>> > >> http://tr.im/mikes_public_calendar
>> > >>
>> > >> ~ Certainty is folly... I think. ~
>> > >
>> > >
>> >
>> >
>> >
>> > --
>> > Mike Lawrence
>> > Graduate Student
>> > Department of Psychology
>> > Dalhousie University
>> >
>> > Looking to arrange a meeting? Check my public calendar:
>> > http://tr.im/mikes_public_calendar
>> >
>> > ~ Certainty is folly... I think. ~
>
>
>
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